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By means of large-scale atomistic simulations, we identity and characterize several kinds of bonding and coordination defects at the interface between a silicon nanoparticle and an embedding amorphous silicon dioxide matrix. In particular, we prove that interface bond defects are easily formed, while no Si–O double bond is observed. We conclude that optical properties, e.g., photoluminescence, are more likely due to such interface bond structures. Temperature effects on defect population and nature are discussed as well.